Jan. 27th 2015

  • Goal : To identify baseline DNA methylation markers that predict the change in PHQ (Aim 1)

  • Model : PHQchange = a + b * BaselineMethylation + e

  • Sites : 437247

  • Sample size: 65

  • Multiple Testing Correction : Bonferroni

  • 5% MinP Cutoff - Raw PHQchange :

  • 5% MinP Cutoff - INV PHQchange :

Association Test

Raw PHQchange ~ Baseline Methylation

QQplot of pvals based on Raw PHQchange and CI

Results based on Raw PHQchange
CpG Chr Genes Pos beta pval p.adj size
cg25660390 17 NA 73073700 0.003 0.0e+00 0.0039 65
cg07219643 12 WSB2 118499016 0.001 1.0e-07 0.0327 65
cg15286044 10 CRTAC1 99789971 0.004 1.0e-07 0.0381 65
cg23932859 5 MEGF10 126625777 0.008 2.0e-07 0.0989 65
cg23679073 2 ZC3H15 187350909 0.002 3.0e-07 0.1408 65
cg26752884 11 JRKL;CCDC82 96123217 0.002 4.0e-07 0.1802 65
cg04992638 17 LOC100133991;C17orf46 43339328 0.002 4.0e-07 0.1889 65
cg25365565 6 HIST1H2BJ;HIST1H2AG 27101050 0.001 1.0e-06 0.4479 65
cg24190377 17 C17orf101 80350294 -0.001 1.1e-06 0.4659 65
cg22327690 17 TRIM37 57179774 -0.004 1.4e-06 0.6174 65

Studentized Residual QQ plots top 6 sites - raw PHQchange

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63127 
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63127 
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50136 
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63127 
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63127 
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Leverage Plots top 6 sites - raw PHQchange

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Cook's Distance - raw PHQchange

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PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ Baseline Methylation

QQplot of pvals based on INV PHQchange and CI

QQplot: adj by covariates

Results based on INV PHQchange
CpG Chr Genes Pos beta pval p.adj size
cg07219643 12 WSB2 118499016 0.004 1.0e-07 0.0510 65
cg23679073 2 ZC3H15 187350909 0.008 1.0e-07 0.0575 65
cg15286044 10 CRTAC1 99789971 0.013 7.0e-07 0.2946 65
cg00220389 17 NA 80455521 0.006 7.0e-07 0.3118 65
cg07696033 11 ALX4 44326410 0.008 1.1e-06 0.4659 65
cg20696752 17 LSM12 42143797 0.004 1.5e-06 0.6718 65
cg14613271 2 SLC5A7 108602931 0.013 2.2e-06 0.9507 65
cg02592615 6 HIVEP1 12012261 0.010 2.5e-06 1.0000 65
cg07399094 6 NA 3163461 0.007 2.9e-06 1.0000 65
cg26752884 11 JRKL;CCDC82 96123217 0.006 3.0e-06 1.0000 65

Residual QQ plots top 6 sites - INV PHQchange

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63127 
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63127 
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63127 
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Leverage Plots top 6 sites - INV PHQchange

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Cook's Distance - INV PHQchange

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PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ INV Baseline Methylation

QQplot pvals : INV PHQchange ~ INV Base Methylation

ScatterPlot: -log10 InvDiffMethyl vs -log10 DiffMethyl

Results based on INV PHQchange ~ INV Base Methylation
CpG Chr Genes Pos beta pval p.adj size
cg23679073 2 ZC3H15 187350909 0.183 1.0e-07 0.0436 65
cg21746851 3 PRRT3 9994105 -0.108 6.0e-07 0.2714 65
cg08099331 16 DEXI;CLEC16A 11037187 -0.150 8.0e-07 0.3411 65
cg26719995 2 EMILIN1;KHK 27309153 -0.080 1.4e-06 0.6246 65
cg22327690 17 TRIM37 57179774 -0.105 2.5e-06 1.0000 65
cg09984518 19 AKAP8L 15529851 0.240 3.8e-06 1.0000 65
cg17006519 13 HNRNPA1L2 53191650 -0.040 6.0e-06 1.0000 65
cg20883684 2 C1QL2 119917385 0.108 6.5e-06 1.0000 65
cg14020595 4 SPATA5 124234087 -0.114 6.7e-06 1.0000 65
cg19156280 3 NGLY1 25825111 0.132 7.6e-06 1.0000 65

Residual QQ plots top 6 sites

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Leverage Plots top 6 sites

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Cook's Distance : INV PHQchange ~ INV Base Methylation

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PCA on top sites - Scree Plot

PCA on top sites - biplot